Optimization by simulating molecular evolution

Based on the analogy between mathematical optimization and molecular evolution and on Eigen's quasi-species model of molecular evolution, an evolutionary algorithm for combinatorial optimization has been developed. This algorithm consists of a versatile variation scheme and an innovative decision rule, the essence of which lies in a radical revision of the conventional philosophy of optimization: A number of configurations of variables with better values, instead of only a single best configuration, are selected as starting points for the next iteration. As a result the search proceeds in parallel along a number of routes and is unlikely to get trapped in local optima. An important innovation of the algorithm is introduction of a constraint to let the starting points always keep a certain distance from each other so that the search is able to cover a larger region of space effectively. The main advantage of the algorithm is that it has more chances to find the global optimum and as many local optima as possible in a single run. This has been demonstrated in preliminary computational experiments.     

Growth and death in overagitated microcarrier cell cultures

The effects of hydrodynamic forces on cell growth are investigated for animal cells growing on microcarriers. A reduction in net growth was observed with high levels of agitation. DNA measurements indicated that the reduction in net growth was due entirely to cell death, from hydrodynamic forces. No inhibition or enhancement of cell replication appeared to occur with high levels of agitation.     

The cytogenetics of domestic geese

Hybrids were produced between an African male and several Pilgrim female domestic geese. Partial karyotypes revealed a difference in the fourth largest pair of autosomal chromosomes. This chromosome pair was metacentric in the African, submetacentric in the Pilgrim, and heteromorphic in the hybrids. A similar difference between the putative wild ancestors of the African and Pilgrim breeds has been reported by others. These findings provide cytological evidence to support the traditional opinion that the African breed was derived from the Asiatic swan goose (Anser cygnoides) and the Pilgrim breed was derived from the European greylag goose (Anser anser).     

Identification of a pterin derivative in Escherichia coli DNA photolyase

DNA photolyase from Escherichia coli contains reduced flavin adenine dinucleotide plus a second chromophore, partially characterized in previous studies. Both chromophores function as sensitizers in catalysis. The second chromophore has been identified as a 6-substituted pterin derivative. The compound is oxidized with permanganate to yield 6-carboxypterin or reduced with sodium cyanoborohydride to yield a 5,6,7,8-tetrahydropterin derivative. The second chromophore exhibits spectral properties (lambda max = 360, 255 nm, pH 2) similar to that observed for 7,8-dihydropterin cations. The compound does not exhibit a spectrally detectable pKa around 4 but is converted to a dication (lambda max = 346, 255 nm) in strong acid (pKa approximately 1). Similar ionization behavior is observed with 7,8-dihydropterin derivatives that are alkylated at N(5). The instability of the second chromophore in weakly alkaline solution is due to a fully reversible conversion to a labile bleached form. As compared with other pterin derivatives, the hydrolytic instability is unusual but is very similar to that observed for 5,6-dialkyl-7,8-dihydropterinium salts. It is proposed that the second chromophore is a 7,8-dihydropterin with substituents at positions 5 and 6. The discovery that a pterin derivative functions as a photosensitizer in DNA repair is apparently the first example of a photobiological function for pterins.     

Resolution of end-to-end distance distributions of flexible molecules using quenching-induced variations of the Forster distance for fluorescence energy transfer.

We describe a new method to recover the distribution of donor-to-acceptor (D-A) distances in flexible molecules using steady-state measurements of the efficiency of fluorescence energy transfer. The method depends upon changes in the Forster distance (Ro) induced by collisional quenching of the donor emission. The Ro-dependent transfer efficiencies are analyzed using nonlinear least squares to recover the mean D-A distance and the width of the distribution. The method was developed and tested using three synthetic D-A pairs, in which the chromophores were separated by alkyl chains of varying lengths. As an example application we also recovered the distribution of distances from the single tryptophan residue in troponin I (trp 158) to acceptor-labeled cysteine 133. The half-width of the distribution increases from 12 A in the native state to 53 A when unfolded by guanidine hydrochloride. For both TnI and the three model compounds the distance distributions recovered from the steady-state transfer efficiencies were in excellent agreement with the distributions recovered using the more sophisticated frequency-domain method (Lakowicz, J.R., M.L. Johnson, W. Wiczk, A. Bhat, and R.F. Steiner. 1987. Chem. Phys. Lett. 138:587-593). The method was found to be reliable and should be generally useful for studies of conformational distributions of macromolecules.     

Chronic measurement, using a Doppler probe, of uterine artery flow in the gravid guinea-pig

A chronic animal model is described which permits for the first time the continuous measurement of uterine artery blood flow velocity in the pregnant guinea-pig by using a miniaturized Doppler flow probe. Preliminary validation revealed that alterations in actual blood flow are directly and proportionally related to the change in the Doppler shift (r = 0.984) from 0 to 100 ml/h. The velocity signal baseline was as stable as that of systemic blood pressure. Depending upon the individual animal's flow velocity, a deviation of 2-5% from baseline was statistically significant. With experience, greater than 90% of preparations were successful and a 30-day interval was often available for study. Uterine artery flow velocity increased steadily between 45 and 55 days of gestation. Instrumentation did not result in fetal growth retardation. A reduction in flow velocity occurred during general anaesthesia using ketamine and the antianxietal xylazine. In agreement with the reports of other investigators using a different model, both hydralazine and angiotensin II increased uterine blood velocity and adrenaline reduced it.